The montmorillonite colloid is an important part of the drilling fluid system. However, the calcium contamination in reservoir can lead to severe aggregation of montmorillonite colloids, which challenges the application of drilling fluid systems in reservoirs with high salinity. To provide insight into the calcium-induced aggregation of montmorillonite colloids, in this work, all-atom molecular dynamics (MD) simulations were adopted to study the morphology and stability of montmorillonite colloid in calcium ion environment, and the cases of ion-free, sodium, and potassium were also considered as comparison. Our simulations demonstrated that montmorillonite particles could agglomerate in three modes: edge-to-edge agglomeration (EEA), partial face-to-face agglomeration (PFFA), and face-to-face agglomeration (FFA). The EEA and PFFA modes were observed in all models, but the FFA mode was the characteristic agglomeration morphology of montmorillonite particles under the effect of Ca2+, which provides implications for the failure of the drilling fluid systems due to calcium contamination. Furthermore, molecular mechanisms underlying the calcium-induced aggregation montmorillonite colloids were investigated. Firstly, the strong electrostatic attraction of Ca2+ enhanced the binding, while the relatively large hydrated radius of Ca2+ allowed increased interlayer space and reduced repulsion. Secondly, the monolayer arrangement and pronounced hydration of Ca2+ led to the elimination of multi-layer cation repulsion and an increase in hydration-induced cohesion. These results extending our knowledge of the stability of montmorillonite colloids present a supplementary perspective to the DLVO theory and will serve as a valuable reference and inspiration for future research on montmorillonite colloid.